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[bioontology-support] [BioPortal] Feedback from Peter Lamb

Lamb, Peter Lamb at nccn.org
Fri Apr 7 10:05:03 PDT 2017


Hi Jennifer!

I happen to know the NCI Thesaurus ontology maintainers quite well as we work closely with them :) I’ve cc’d them on this e-mail – Larry, Margaret, and Sherri.

Larry, can you follow the e-mail chain below and look into the FTP site/pull URL issue that Jennifer mentioned? I think we might have found the source of the problem!

Hopefully we all can work together to sync up NCI Thesaurus and BioPortal!

Peter

Peter Lamb
Medical Informaticist
National Comprehensive Cancer Network® (NCCN®)
275 Commerce Drive  Suite 300  Fort Washington, PA 19034
Phone: 267.628.3366 | Fax: 215.690.0283 | E-mail: lamb at nccn.org<mailto:lamb at nccn.org>

NCCN.org<http://nccn.org/> – For Clinicians | NCCN.org/patients<http://www.nccn.org/patients> – For Patients


From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Friday, April 7, 2017 12:54 PM
To: NCBO User Support <support at bioontology.org>
Cc: Lamb, Peter <Lamb at nccn.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Peter Lamb

Hi Peter,


On Apr 7, 2017, at 8:51 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Peter Lamb
Email: Lamb at nccn.org<mailto:Lamb at nccn.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:
Hi BioPortal team!
I had a question regarding the version of NCI Thesaurus found through BioPortal. It appears that the two latest uploads of NCI Thesaurus have the same version number on BioPortal -- 16.05e, but have two different upload dates (March 2017 and July 2016). Has NCI Thesaurus been updated in BioPortal, or is BioPortal still working off of the July 2016 version of NCI Thesaurus?



I downloaded the OWL file associated with the latest upload (March 2017).  In the ontology file, the dc:date attribute is May 31, 2016.



I also understand that NCI Thesaurus publishes new versions of their terminology on a monthly cycle. Is BioPortal in sync with NCI Thesaurus’s schedule? Does BioPortal grab and load the OWL file at NCI Thesaurus’s time of publication each month?



When end users submit ontologies, they have the option to specify a “pull URL”.  If specified, the BioPortal software will check this URL on a nightly basis for new versions of the ontology.  I looked at the submission properties for NCIT.  They specified an FTP site for their pull URL.  So, it appears that whenever a new version is published to that FTP site, BioPortal retrieves it.  Retrieval is happening fairly infrequently, so it doesn’t seem like this FTP site is the same thing as the monthly releases that you mention above.

I will forward your inquiry to the ontology maintainers to see if they can shed any light on why this FTP site is not updated on a monthly basis.


Background on myself -- my name is Peter Lamb and I am a medical informatisict at the National Comprehensive Cancer Network. We are working to digitize our clinical practice guidelines, and make extensive use of BioPortal for this.
Should this e-mail go to Mark Musen or Nigam Shah, I’d like to say hello! I am a former Stanford Biomedical Informatics alumnus (I got my masters in the program via the honors cooperative program, so I wasn’t on campus). I took BMI210 and BMI215 quite a few years ago now, back in 2012/2013.
Should BioPortal need a letter of support from NCCN for any grant funding, please let me know and I’d be happy to facilitate that from my end. We love the work you’re doing!



I don’t think Drs. Shah or Musen monitor this list.  I’ll forward your message to them.

Kind regards,
Jennifer

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